PDB Download
v1.0.0Fetch experimental structure files from RCSB PDB or PDBe using a PDB ID.
Fetch experimental structure files from RCSB PDB or PDBe using a PDB ID.
ProteinIQ retrieves experimental structure files from RCSB PDB or PDBe using a known structure ID such as 1CRN, 4HHB, or 1Q0L. Enter the four-character ID, choose a source, then select PDB, mmCIF, FASTA (RCSB only), or all formats, then download the returned coordinate or sequence files for inspection, conversion, or downstream analysis.
For 1CRN with PDB source set to RCSB PDB and Output format set to All formats, the file list returns these filenames:
rcsb-1CRN-pdb.pdb
rcsb-1CRN-cif.cif
rcsb-1CRN-fasta.fastaWith PDBe selected, the same ID returns:
pdbe-1CRN-pdb.pdb
pdbe-1CRN-cif.cifPDB Download is a direct-retrieval tool for archived macromolecular structure records in the worldwide Protein Data Bank archive through RCSB PDB or PDBe. Given a known four-character PDB identifier, it retrieves the entry coordinate files and its structure-associated polymer sequences in formats commonly needed for structural biology workflows.
The tool downloads the deposited archive entry, not a predicted structure, a prepared receptor, or a biological assembly. For example, 4HHB retrieves the archived hemoglobin entry files. Experimental method, resolution, missing residues, alternate conformations, chain composition, ligands, and assembly annotations remain properties of that deposited record and should be reviewed on its RCSB entry page before scientific interpretation.
PDBx/mmCIF is the current archival coordinate format and is generally the best choice for new analysis pipelines. Legacy PDB remains useful for software that requires its fixed-column syntax, but it has format limits and will not be available for every future archive entry.
| Field | Description |
|---|---|
Entry ID | A released, four-character PDB identifier. Letter case is accepted, so 4hhb and 4HHB refer to the same entry. This tool retrieves one known record and does not search by protein name, gene, ligand, or UniProt accession. |
| Setting | Description |
|---|---|
Database | PDB by default. Opens another retained download tool: AlphaFold Database, UniProt, PubChem, ChEMBL, or Rhea. |
PDB source | RCSB PDB by default, or PDBe. Both serve the same archive entries through their own file services. PDBe returns PDB and mmCIF; FASTA is available through RCSB. |
Output format | All formats (default) returns PDB and mmCIF, plus FASTA when the source is RCSB PDB. Select PDB, mmCIF, or FASTA to retrieve only that representation. |
An unknown, withdrawn, unreleased, or malformed identifier returns an entry-not-found result. The tool does not infer an ID from a protein name, so use the RCSB PDB search service first when the archive identifier is not known.
| Result item | Extension | Contents | Appropriate use |
|---|---|---|---|
PDB | .pdb | Deposited coordinates in the legacy PDB text format. | A viewer, script, or established method that explicitly requires PDB input. |
CIF | .cif | Deposited coordinates and PDBx/mmCIF data categories. | Modern structure software, larger or more complex entries, and workflows that need the fuller archive representation. |
FASTA | .fasta | Full deposited polymer sequences associated with the PDB entry. | Sequence search, alignment, construct comparison, or sequence-based analysis. |
The file list keeps each selected format separate. Download names are normalized as rcsb-<entry-id>-<format>.<extension>, for example rcsb-4HHB-cif.cif and rcsb-4HHB-fasta.fasta.
The PDB and mmCIF files represent the same deposited entry, but they are not interchangeable formats. Choose mmCIF whenever the next program supports it. It carries the PDBx data model used by the archive and avoids legacy PDB field limitations. Choose PDB only when compatibility with a particular program or script is the deciding factor.
FASTA describes the deposited polymer sequence, which can include residues not resolved as coordinates in the experiment. It is therefore not necessarily the same as the residue set visible in a coordinate file. To extract observed residues, choose chains, or control how missing residues are represented after downloading, use PDB to FASTA.
PDB Download returns the archive entry coordinates, not a biological assembly file. An asymmetric unit can differ from the biologically relevant assembly, particularly for multimeric proteins. When assembly state, experimental quality, or ligand context matters, inspect the corresponding RCSB record and retain the exact file choice with the analysis.
Coordinate files often need preparation for the next scientific question. Use PDB to CIF when a PDB-only source must be converted for an mmCIF-capable workflow. Use PDB Fixer when a modeling or simulation workflow needs a cleaned structure with decisions about missing atoms, residues, or heterogens made explicitly.
PDBe is the European partner of the worldwide PDB archive. Use PDB source to choose PDBe without opening a separate tool. The entry ID is shared, but source URLs, filenames, and delivered file details remain source-specific. ProteinIQ does not silently switch sources if a download fails.
The PDBe option in this tool provides coordinate files only. Switch PDB source to RCSB PDB for FASTA, or select PDB or mmCIF while staying on PDBe.
Enter one identifier or compound name on a single line, up to 200 characters. Surrounding spaces are ignored. These lookups need an internet connection: ProteinIQ retrieves the record from the selected database, and file downloads contact its file service.
If a text file cannot be loaded in the browser, a warning appears and its download link stays available. A listed link does not guarantee that the database currently serves that file. Retry the download or check the original database record; a connection failure is different from an unknown entry.
Fetch AlphaFold DB CIF, PDB, BCIF, and PAE JSON files from a UniProt accession.
Fetch UniProt protein sequence files, JSON records, and available sequence content by accession.
Fix PDB and mmCIF structures by adding missing atoms, residues, hydrogens, and solvent.
Convert PDB coordinates to mmCIF with model selection and warnings for omitted records.
Extract observed or full SEQRES sequences from PDB structures with chain selection and RCSB fetching.
Fetch ChEMBL compound structure and metadata files by ChEMBL molecule ID.
Convert CSV or TSV sequence tables to FASTA with automatic delimiter detection and column mapping.
Paste or upload a sequence file in any common format and download FASTA. The format is detected automatically, and nothing leaves your browser.
Split FASTA records by count, target file count, record length, or one sequence per file.
Paste or upload FASTA and download a CSV or TSV table for spreadsheets, or a plain text file with one sequence per line.